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Vol. 12, Issue 2, 323-337, February 2001

Remodeling of Yeast Genome Expression in Response to Environmental Changes

Helen C. Causton,*dagger Dagger Bing Ren,*dagger Sang Seok Koh,*§ Christopher T. Harbison,*|| Elenita Kanin,* Ezra G. Jennings,*|| Tong Ihn Lee,*|| Heather L. True, Eric S. Lander,*|| and Richard A. Young*||#

 *Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142;  ||Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; and  Howard Hughes Medical Institute, Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637

We used genome-wide expression analysis to explore how gene expression in Saccharomyces cerevisiae is remodeled in response to various changes in extracellular environment, including changes in temperature, oxidation, nutrients, pH, and osmolarity. The results demonstrate that more than half of the genome is involved in various responses to environmental change and identify the global set of genes induced and repressed by each condition. These data implicate a substantial number of previously uncharacterized genes in these responses and reveal a signature common to environmental responses that involves ~10% of yeast genes. The results of expression analysis with MSN2/MSN4 mutants support the model that the Msn2/Msn4 activators induce the common response to environmental change. These results provide a global description of the transcriptional response to environmental change and extend our understanding of the role of activators in effecting this response.


dagger These authors made equal contributions.

Present addresses: Dagger MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Campus, Du Cane Road, London W12 ONN, UK; §LG Chemical Ltd., Research Park, 104-1, Moon Ji-Dong, Song-Gu, Taejon, Korea.

# Corresponding author. E-mail address: young{at}WI.MIT.EDU.


Molecular Biology of the Cell
Vol. 12, 323-337, February 2001
Copyright © 2001 by The American Society for Cell Biology



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Mol. Cell. Biol., November 1, 2005; 25(21): 9447 - 9459.
[Abstract] [Full Text] [PDF]


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Eukaryot CellHome page
V. K. Vyas, C. D. Berkey, T. Miyao, and M. Carlson
Repressors Nrg1 and Nrg2 Regulate a Set of Stress-Responsive Genes in Saccharomyces cerevisiae
Eukaryot. Cell, November 1, 2005; 4(11): 1882 - 1891.
[Abstract] [Full Text] [PDF]


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Mol. Cell. Biol.Home page
C. Conesa, R. Ruotolo, P. Soularue, T. A. Simms, D. Donze, A. Sentenac, and G. Dieci
Modulation of Yeast Genome Expression in Response to Defective RNA Polymerase III-Dependent Transcription
Mol. Cell. Biol., October 1, 2005; 25(19): 8631 - 8642.
[Abstract] [Full Text] [PDF]


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Mol. Biol. CellHome page
M. P. Nittler, D. Hocking-Murray, C. K. Foo, and A. Sil
Identification of Histoplasma capsulatum Transcripts Induced in Response to Reactive Nitrogen Species
Mol. Biol. Cell, October 1, 2005; 16(10): 4792 - 4813.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
S. Vanderauwera, P. Zimmermann, S. Rombauts, S. Vandenabeele, C. Langebartels, W. Gruissem, D. Inze, and F. Van Breusegem
Genome-Wide Analysis of Hydrogen Peroxide-Regulated Gene Expression in Arabidopsis Reveals a High Light-Induced Transcriptional Cluster Involved in Anthocyanin Biosynthesis
Plant Physiology, October 1, 2005; 139(2): 806 - 821.
[Abstract] [Full Text] [PDF]


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Genome ResHome page
A. A. Petti and G. M. Church
A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae
Genome Res., September 1, 2005; 15(9): 1298 - 1306.
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J. Biol. Chem.Home page
I. Bourges, S. Horan, and B. Meunier
Effect of Inhibition of the bc1 Complex on Gene Expression Profile in Yeast
J. Biol. Chem., August 19, 2005; 280(33): 29743 - 29749.
[Abstract] [Full Text] [PDF]


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Mol. Cell. Biol.Home page
K. Rothfels, J. C. Tanny, E. Molnar, H. Friesen, C. Commisso, and J. Segall
Components of the ESCRT Pathway, DFG16, and YGR122w Are Required for Rim101 To Act as a Corepressor with Nrg1 at the Negative Regulatory Element of the DIT1 Gene of Saccharomyces cerevisiae
Mol. Cell. Biol., August 1, 2005; 25(15): 6772 - 6788.
[Abstract] [Full Text] [PDF]


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Eukaryot CellHome page
D. J. Krysan, E. L. Ting, C. Abeijon, L. Kroos, and R. S. Fuller
Yapsins Are a Family of Aspartyl Proteases Required for Cell Wall Integrity in Saccharomyces cerevisiae
Eukaryot. Cell, August 1, 2005; 4(8): 1364 - 1374.
[Abstract] [Full Text] [PDF]


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Eukaryot CellHome page
S. Claret, X. Gatti, F. Doignon, D. Thoraval, and M. Crouzet
The Rgd1p Rho GTPase-Activating Protein and the Mid2p Cell Wall Sensor Are Required at Low pH for Protein Kinase C Pathway Activation and Cell Survival in Saccharomyces cerevisiae
Eukaryot. Cell, August 1, 2005; 4(8): 1375 - 1386.
[Abstract] [Full Text] [PDF]


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GeneticsHome page
N. Bing and I. Hoeschele
Genetical Genomics Analysis of a Yeast Segregant Population for Transcription Network Inference
Genetics, June 1, 2005; 170(2): 533 - 542.
[Abstract] [Full Text] [PDF]


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Mol. Cell. Biol.Home page
L.-C. Lai, A. L. Kosorukoff, P. V. Burke, and K. E. Kwast
Dynamical Remodeling of the Transcriptome during Short-Term Anaerobiosis in Saccharomyces cerevisiae: Differential Response and Role of Msn2 and/or Msn4 and Other Factors in Galactose and Glucose Media
Mol. Cell. Biol., May 15, 2005; 25(10): 4075 - 4091.
[Abstract] [Full Text] [PDF]


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Mol. Cell. Biol.Home page
C. Tachibana, J. Y. Yoo, J.-B. Tagne, N. Kacherovsky, T. I. Lee, and E. T. Young
Combined Global Localization Analysis and Transcriptome Data Identify Genes That Are Directly Coregulated by Adr1 and Cat8
Mol. Cell. Biol., March 15, 2005; 25(6): 2138 - 2146.
[Abstract] [Full Text] [PDF]


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Appl. Environ. Microbiol.Home page
J. Panadero, F. Randez-Gil, and J. A. Prieto
Validation of a Flour-Free Model Dough System for Throughput Studies of Baker's Yeast
Appl. Envir. Microbiol., March 1, 2005; 71(3): 1142 - 1147.
[Abstract] [Full Text] [PDF]


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GeneticsHome page
S. Bose, J. A. Dutko, and R. S. Zitomer
Genetic Factors That Regulate the Attenuation of the General Stress Response of Yeast
Genetics, March 1, 2005; 169(3): 1215 - 1226.
[Abstract] [Full Text] [PDF]


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GeneticsHome page
S. B. Ferguson, E. S. Anderson, R. B. Harshaw, T. Thate, N. L. Craig, and H. C. M. Nelson
Protein Kinase A Regulates Constitutive Expression of Small Heat-Shock Genes in an Msn2/4p-Independent and Hsf1p-Dependent Manner in Saccharomyces cerevisiae
Genetics, March 1, 2005; 169(3): 1203 - 1214.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
Y. Garten, S. Kaplan, and Y. Pilpel
Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data
Nucleic Acids Res., January 31, 2005; 33(2): 605 - 615.
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J. Biol. Chem.Home page
J. Zaim, E. Speina, and A. M. Kierzek
Identification of New Genes Regulated by the Crt1 Transcription Factor, an Effector of the DNA Damage Checkpoint Pathway in Saccharomyces cerevisiae
J. Biol. Chem., January 7, 2005; 280(1): 28 - 37.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
E. Durchschlag, W. Reiter, G. Ammerer, and C. Schuller
Nuclear Localization Destabilizes the Stress-regulated Transcription Factor Msn2
J. Biol. Chem., December 31, 2004; 279(53): 55425 - 55432.
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Eukaryot CellHome page
M. Krantz, B. Nordlander, H. Valadi, M. Johansson, L. Gustafsson, and S. Hohmann
Anaerobicity Prepares Saccharomyces cerevisiae Cells for Faster Adaptation to Osmotic Shock
Eukaryot. Cell, December 1, 2004; 3(6): 1381 - 1390.
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GeneticsHome page
J. W. Loar, R. M. Seiser, A. E. Sundberg, H. J. Sagerson, N. Ilias, P. Zobel-Thropp, E. A. Craig, and D. E. Lycan
Genetic and Biochemical Interactions Among Yar1, Ltv1 and RpS3 Define Novel Links Between Environmental Stress and Ribosome Biogenesis in Saccharomyces cerevisiae
Genetics, December 1, 2004; 168(4): 1877 - 1889.
[Abstract] [Full Text] [PDF]


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Mol. Biol. CellHome page
B. Schade, G. Jansen, M. Whiteway, K. D. Entian, and D. Y. Thomas
Cold Adaptation in Budding Yeast
Mol. Biol. Cell, December 1, 2004; 15(12): 5492 - 5502.
[Abstract] [Full Text] [PDF]


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Proc. Natl. Acad. Sci. USAHome page
S. J. Zanton and B. F. Pugh
Changes in genomewide occupancy of core transcriptional regulators during heat stress
PNAS, November 30, 2004; 101(48): 16843 - 16848.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
L. Viladevall, R. Serrano, A. Ruiz, G. Domenech, J. Giraldo, A. Barcelo, and J. Arino
Characterization of the Calcium-mediated Response to Alkaline Stress in Saccharomyces cerevisiae
J. Biol. Chem., October 15, 2004; 279(42): 43614 - 43624.
[Abstract] [Full Text] [PDF]


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Proc. Natl. Acad. Sci. USAHome page
R. M. Marion, A. Regev, E. Segal, Y. Barash, D. Koller, N. Friedman, and E. K. O'Shea
Inaugural Article: Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression
PNAS, October 5, 2004; 101(40): 14315 - 14322.
[Abstract] [Full Text] [PDF]


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MicrobiologyHome page
L. Wang, G. Renault, H. Garreau, and M. Jacquet
Stress induces depletion of Cdc25p and decreases the cAMP producing capability in Saccharomyces cerevisiae
Microbiology, October 1, 2004; 150(10): 3383 - 3391.
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Eukaryot CellHome page
S. Nicholls, M. Straffon, B. Enjalbert, A. Nantel, S. Macaskill, M. Whiteway, and A. J. P. Brown
Msn2- and Msn4-Like Transcription Factors Play No Obvious Roles in the Stress Responses of the Fungal Pathogen Candida albicans
Eukaryot. Cell, October 1, 2004; 3(5): 1111 - 1123.
[Abstract] [Full Text] [PDF]


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Eukaryot CellHome page
K. A. Kafadar and M. S. Cyert
Integration of Stress Responses: Modulation of Calcineurin Signaling in Saccharomyces cerevisiae by Protein Kinase A
Eukaryot. Cell, October 1, 2004; 3(5): 1147 - 1153.
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Mol. Biol. CellHome page
D. A. Smith, S. Nicholls, B. A. Morgan, A. J.P. Brown, and J. Quinn
A Conserved Stress-activated Protein Kinase Regulates a Core Stress Response in the Human Pathogen Candida albicans
Mol. Biol. Cell, September 1, 2004; 15(9): 4179 - 4190.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
T. B. Salmon, B. A. Evert, B. Song, and P. W. Doetsch
Biological consequences of oxidative stress-induced DNA damage in Saccharomyces cerevisiae
Nucleic Acids Res., July 14, 2004; 32(12): 3712 - 3723.
[Abstract] [Full Text] [PDF]




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